Sequence
atgc intronic sequence ATGC exonic sequencegtactgcttaaaagttttgagagttttttttcatggttttttttctctcttgggtgatttttccgtccttggatctggatggtgtttttggtgtggtacttgatccatcctccagtgtacttaggtgagtaatctatcgaatttttctcgattgtggagctaaacttttggtggttttctttgcgttttgcgtagGGGGATATGATGCGGAGGAGAAGGCAGCAAGAGCTTACGATCTGGCAGCTCTCAAGTACTGGGGGCCTACGACAACTACAAACTTTCCG
Basic information
species | Selaginella moellendorffii |
transcript | EFJ16224 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ16224 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os06g44750.1 (Oryza sativa), 3'ss of exon 4
gtactgcttaaaagttttgagagttttttttcatggttttttttctctcttgggtgatttttccgtccttggatctggatggtgtttttggt-gtggtacttgatccatcctccagtgtacttaggtgagtaatctatcgaatttttctcgattgtggagctaaacttttggtggttttctttgcgttttgcgtagGGGGATATGATGCGGAGGAGAAGGCAGCAAGAGCTTACGATCTGGCAGCTCTCAAGTACTGGGGGCCTACGACAACTACAAACTTTCCG
| ||| || || | | | | || ||| | | | || |||| | | | ||| || || || | |||| || || | || ||| ||| || |||||| |||||||||||| |||||||||||||| || || || || ||||||||||| || || || || || ||||| ||
----------------------------------------------------------------------------gtatgtcgtcattatttgcaacatct-atatatctt--aat-tagttagtttcttttccattcg--ttcaccttgagacttactgtaaaagttgggggattaaacaaaactttc----agGAGGTTATGATAAGGAGGAGAAGGCCGCAAGAGCTTACGACCTCGCCGCCCTAAAGTACTGGGGTCCAACCACCACGACGAACTTCCCT
upper sequence: EFJ16224 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G366434_T01 (Zea mays), 3'ss of exon 3
gtactgcttaaaagttttgagagttttttttcatggttttttttctctcttgggtgatttttccgtccttggatctggatggtgtttttggtgtggtacttgatccatcctccagtgtacttaggtgagtaatctatcgaatttttctcgattgtggagctaaacttttggtggttttctttgcgttttgcgtagGGGGATATGATGCGGAGGAGAAGGCAGCAAGAGCTTACGATCTGGCAGCTCTCAAGTACTGGGGGCCTACGACAACTACAAACTTTCCG
||| || || | | | || || | | ||| || | |||| | | |||| | || | |||| | ||| | || | | |||| || ||||| |||||| ||||||||||| ||||||||| |||||||||||||||| ||||| |||||||||| ||||| || ||
---------------------------------------------------------------------------tggt--atgcattcaccttagctcctg-cccttacatttttgttgttgtatag---atcttccta--ttttaacaatcattttgctatgccattgtatatccactgtaTACACT---TAGGTGGCTATGACAAGGAGGACAAGGCAGCAAGGGCTTACGATTTGGCAGCTCTCAAGTATTGGGGCACTACGACAACAACAAATTTCCCT
upper sequence: EFJ16224 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G366434_T02 (Zea mays), 3'ss of exon 3
gtactgcttaaaagttttgagagttttttttcatggttttttttctctcttgggtgatttttccgtccttggatctggatggtgtttttggtgtggtacttgatccatcctccagtgtacttaggtgagtaatctatcgaatttttctcgattgtggagctaaacttttggtggttttctttgcgttttgcgtagGGGGATATGATGCGGAGGAGAAGGCAGCAAGAGCTTACGATCTGGCAGCTCTCAAGTACTGGGGGCCTACGACAACTACAAACTTTCCG
|| | | || || | | | || || | | ||| || | |||| | | |||| | || | |||| | ||| | || | | |||| || ||||| |||||| ||||||||||| ||||||||| |||||||||||||||| ||||| |||||||||| ||||| || ||
--------------------------------------------------------------------------cttggta-tgcattcaccttagctcctg-cccttacatttttgttgttgtatag---atcttccta--ttttaacaatcattttgctatgccattgtatatccactgTATACACT---TAGGTGGCTATGACAAGGAGGACAAGGCAGCAAGGGCTTACGATTTGGCAGCTCTCAAGTATTGGGGCACTACGACAACAACAAATTTCCCT
upper sequence: EFJ16224 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G139082_T01 (Zea mays), 3'ss of exon 4
gtactgcttaaaagttttgagagttttttttcatggttttttttctctcttgggtgatttttccgtccttggatctggatggtgtttttggtgtggt--acttgatccatcctccagtgtacttaggtgagtaatctatcgaatttttctcgattgtggagctaaacttttggtggttttctttgcgttttgcgtagGGGGATATGATGCGGAGGAGAAGGCAGCAAGAGCTTACGATCTGGCAGCTCTCAAGTACTGGGGGCCTACGACAACTACAAACTTTCCG
|| | | | | | | || | | ||||| | || | | || | | || | ||| | | | |||| || | || || | | ||| ||| |||| | || | ||||| || ||||| |||||||||||| || ||||||||||| || || || |||||||||||||||||||| || || || ||||| |||
----------------------gtacgtatatactacgtcaacttccactacacccagtactccgtttcagcttcagttggacacttacattcaaatcaacattatcaaatcaa-aatgtatttttttagatatattagaaagtgttt---------ggaactaactgtggaaaggg-------ggaaaaactgtagGAGGCTATGACAAGGAGGAGAAGGCGGCTAGAGCTTACGACCTCGCCGCGCTCAAGTACTGGGGGCCTACAACCACGACCAACTTCCCG
upper sequence: EFJ16224 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G399072_T01 (Zea mays), 3'ss of exon 3
gtactgcttaaaagttttgagagttttttttcatggttttttttctctcttgggtgatttttccgtccttggatctggatggtgtttttggtgtggtacttgatccatcctccagtgtacttaggtgagtaatctatcgaatttttctcgattgtggagctaaacttttgg---tggttttctttgcgttttgcgtagGGGGATATGATGCGGAGGAGAAGGCAGCAAGAGCTTACGATCTGGCAGCTCTCAAGTACTGGGGGCCTACGACAACTACAAACTTTCCG
| | || | | ||| || | || || | ||| | | | ||| | | | | | | | || | | |||| || ||||| |||||||||||| || || ||||| || ||||||||||||||||||||||| || |||| | ||| || |||
--------------------------------------------------------------------------------------tcaacaacgacgagcagtctaccta--ggtgagctactgcaagcctcctcctagctgtttgttgctccacatgctcaccaccatgtctttgctatgactgtgGCTGCTCTAGGCGGCTATGACAGGGAGGAGAAGGCTGCGAGGGCTTATGACCTGGCAGCTCTCAAGTACTGGGGCCCCTCGACTCACATAAATTTCCCG
upper sequence: EFJ16224 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G399072_T03 (Zea mays), 3'ss of exon 3
gtactgcttaaaagttttgagagttttttttcatggttttttttctctcttgggtgatttttccgtccttggatctggatggtgtttttggtgtggtacttgatccatcctccagtgtacttaggtgagtaatctatcgaatttttctcgattgtggagctaaa---cttttggtggttttctttgcgttttgcgtagGGGGATATGATGCGGAGGAGAAGGCAGCAAGAGCTTACGATCTGGCAGCTCTCAAGTACTGGGGGCCTACGACAACTACAAACTTTCCG
||| || | || || | ||| | | | ||| | | | | | | | | || | | |||| || ||||| |||||||||||| || || ||||| || ||||||||||||||||||||||| || |||| | ||| || |||
------------------------------------------------------------------------------------------------------------------gtgagctactgcaagcctcctcctagctgtttgttgctccacatgctcaccaccatgtctttgctatgactgtggctgctctagGCGGCTATGACAGGGAGGAGAAGGCTGCGAGGGCTTATGACCTGGCAGCTCTCAAGTACTGGGGCCCCTCGACTCACATAAATTTCCCG
upper sequence: EFJ16224 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA17G07010.1 (Glycine max), 3'ss of exon 4
gtactgcttaaaagttttgagagttttttttcatggttttttttctctcttgggtgatttttccgtccttggatctggatggtgtttttggtgtggtacttgatccatcctccagtgtacttaggtgagtaatctatcgaatttttctcgattgtggagctaaacttttggtggttttctttgcgttttgcgtagGGGGATATGATGCGGAGGAGAAGGCAGCAAGAGCTTACGATCTGGCAGCTCTCAAGTACTGGGGGCCTACGACAACTACAAACTTTCCG
| ||| | | ||| | | ||| | | ||| || || | | | ||| | | || ||||| |||| || | | ||| |||| ||| |||| || ||||| |||||| |||||||| |||||||| ||||| |||||||||||||||||||| || || || || || ||||||||
---------------------------------------------------------------------------ttgattgcgcattt--cctagattcagattc-ttctctaggataatcattttagtcaaaaaatgactttttt---gttgt----------ttcttcttcctttttttgtgtt----atagGTGGTTATGACAAGGAGGATAAGGCAGCCAGAGCTTATGATCTCGCAGCTCTCAAGTACTGGGGTCCAACTACCACCACTAACTTTCCT
upper sequence: EFJ16224 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA13G00950.1 (Glycine max), 3'ss of exon 4
gtactgcttaaaagttttgagagttttttttcatggttttttttctctcttgggtgatttttccgtccttggatctggatggtgtttttggtgtggtacttgatccatcctccagtgtacttaggtgagtaatctatcgaatttttctcgattgtggagcta-aacttttggtggtt-ttctttgcgttttgcgtagGGGGATATGATGCGGAGGAGAAGGCAGCAAGAGCTTACGATCTGGCAGCTCTCAAGTACTGGGGGCCTACGACAACTACAAACTTTCCG
|| || | || | || |||| |||| ||| | | | | | | | ||| ||| || | | ||||| | | | | || | | | || | || | | ||||||| | || ||| || | | |||| || ||||| ||| || |||||||| || ||||||||||| |||||||||||||||||||| || || || || || ||||||||
---gtgagtatat-cattactaccttgacctcatcattttgttttaccatcacaaaccacatacatatatacaactgttca---tttatgatcatcaatttgattgcgcatttcccagattcagattcttctctagctaggataatcattttagtcaaaaaatgacttttgtttcttcttccttttctgtgttatagGTGGTTATGACAAGGAAGATAAGGCAGCCAGGGCTTACGATCTCGCAGCTCTCAAGTACTGGGGTCCAACTACCACCACCAACTTTCCC
upper sequence: EFJ16224 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA01G02760.1 (Glycine max), 3'ss of exon 4
gtactgcttaaaagttttgagagttttttttcatggttttttttctctcttgggtgatttttccgtccttggatctggatggtgtttttggtgtggtacttgatccatcctccagtgtacttaggtgagtaatct--atcgaatttttctcgattgtggagctaaacttttggtggttttctttg-cgttttgcgtagGGGGATATGATGCGGAGGAGAAGGCAGCAAGAGCTTACGATCTGGCAGCTCTCAAGTACTGGGGGCCTACGACAACTACAAACTTTCCG
| || | || || | | | | |||| | ||||| | | | ||| ||| | || || | ||| ||| | ||| ||||||||| ||| || ||||| || |||||||| ||| |||||||||| ||||||||||| || || | || || ||||| ||
------------------------------------------------------------------------------------------------catttagatt-tacttcaagaaatctgctcaacttatcttaaaaaaatttatgttgtttg-agagatggttttgtgacatagtaaattgtcgtggttatcagGTGGATATGATAAGGAAGAAAAGGCCGCGAGAGCTTATGATTTGGCAGCTCTAAAGTACTGGGGTCCCACTGCTACCACCAACTTCCCT
upper sequence: EFJ16224 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: Vv11s0052g00840.t01 (Vitis vinifera), 3'ss of exon 4
gtactgcttaaaagttttgagagttttttttcatggttttttttctctcttgggtgatttttccgtcc-ttggatct-ggatggtgtttttggtgtggtacttgatccatcctccagtgtacttagg---tgagtaatctatcgaatttt---tctcgattgtggagctaaacttttggtggttt-tctttgcgttttgcgtagGGGGATATGATGCGGAGGAGAAGGCAGCAAGAGCTTACGATCTGGCAGCTCTCAAGTACTGGGGGCCTACGACAACTACAAACTTTCCG
|| | |||||| | ||| | ||| || | |||| | | | || | | | || || || | |||| | ||| |||| | || |||| | ||| | | | || | | ||| || |||||| ||| ||||||||||| |||||||| ||||| || ||||| ||||||||||| || || || || || ||||| ||
----------------------------------------------------------------gtgagtaggatctcatctcgtggtcttgtcctgaatcatgattt-ttcactgttgaataaaagattctgatattccttcaagttttagattctcattttggatc--aatttttatttatttatttattttttgtttgcagGTGGGTATGATAAGGAAGAGAAGGCAGCTAGAGCTTATGATCTCGCCGCTCTTAAGTACTGGGGTCCGACCACCACCACTAACTTCCCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttttctcgattgtggagctaaacttttggtggttttctttgcgttttgcgtagGGGGATATGATGCGGAGGAGAAGGCAGCAAGAGCTTACGATCTGGCAGCTCTCAAGTACTGGGGGCCTACGACAACTACAAACTTTCCG
agctaaa putative branch site (score: 3)
ttttctttgcgtttt putative PPT
taaactttt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactgcttaaaagttttgagagttttttttcatggttttttttctctcttgggtgatttttccgtccttggatctggatggtgtttttggtgtggtacttgatccatcctccagtgtacttaggtgagtaatctatcgaatttttctcgattgtggagctaaacttttggtggttttctttgcgttttgcgtagGGGGATATGATGCGGAGGAGAAGGCAGCAAGAGCTTACGATCTGGCAGCTCTCAAGTACTGGGGGCCTACGACAACTACAAACTTTCCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC